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<h2><b><a name="DatabaseAccess"></a>Accessing Databases</b></h2>

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<p>One important aspect of <span class="keyword">DataWarrior</span> is its direct access to various
of Actelion's research databases. Queries on these databases may be
composed by specifying search criteria in dedicated dialogs.
Depending on the database the search criteria may consist
of simple criteria as Actelion numbers,
project names, test name, lab journal numbers, experiment dates or
you may define activity thresholds in certain assays or even specify a
certain substructure that retrieved hits are required to contain.<br>
For common search tasks in the <span class="keyword">OSIRIS database</span>, which contains
Actelion's inhouse compounds and their biological assay results, one
may store queries in the database for later reuse. Optionally, stored
queries may be defined as public and therefore wil be available to
other users as well. Database queries may be extended by adding a <i>template</i>.
After a query has been executed, which had a template attached,
predefined views will be generated, labels attached, filters applied,
etc.<br>
OSIRIS queries may also be saved in a local query file. Attaching query
files to an e-mail allows sharing results within the company with
high
degree of confidentiality. These files
always contain a template therefore will automatically reconstruct
all settings after running the query. Query files can only be
run within the Actelion network by an authorized user having an
account to logon to the database. They are very small and do not
contain any data themselves. Furthermore, running a database query
ensures always to work on up-to-date information.</p>
<br>
<h3><i><a name="OsirisCompounds"></a>OSIRIS Compound Information</i></h3>

<p>This interface permits to query the database for chemical compounds that were 
  once registered in the OSIRIS database and therefore have an Actelion number. 
  Selecting <span class="menu">Retrieve Chemical Data...</span> 
  from the <span class="menu">Database / OSIRIS Database</span> 
  menu opens a dialog where you can specify various search criteria as substructure 
  or similarity search, registration project, registration date, etc. If you intend 
  to restrict a search to batches from a specific chemist or producer, then please 
  specify his or her Oracle login ID rather than a full name. If you want different 
  batches with the same structure to be merged into one row, then you need 
  to check <span class="menu">Group Results By Chemical Structure</span>.</p>
<p align="center"><img src="help/img/actelion/OsirisChemQuery.jpg"></p>
<p>If your data contains rows with Actelion numbers, chemical lab journals 
  or Actelion screening library plate positions, but no chemical structures, then 
  you may retrieve the chemical structures from the database by selecting <span class="menu">Retrieve 
  Structures</span> from the <span class="menu">Database / OSIRIS 
  Database</span> menu.</p>
<p>Imagine your current DataWarrior document contains some chemical structures 
  and you would like to know if any of these structures are already registered 
  in the OSIRIS database. You may achieve this with <span class="menu">Find 
  Matching Structures...</span> from the <span class="menu">Database 
  / OSIRIS Database</span> menu, which performs an exact structure search with 
  every one of your compounds against the OSIRIS database and retrieves the associated 
  Actelions numbers into a new column.</p>
<br><br>

<h3><i><a name="OsirisQueries"></a>OSIRIS Biological Query Builder</i></h3>

<p> This interface allows the user to query the database to retrieve project related 
  information. From the <span class="menu">Database</span> menu select <span class="menu">Osiris Database / Retrieve 
  Biological Data</span>. If you are not connected yet, you will be prompted to enter 
  your user name and your password to logon to the database. Then, use the <span class="keyword">OSIRIS 
  Database Query</span> dialog to define your search.</p>

<p align="center"><img src="help/img/actelion/OsirisDatabaseQuery.jpg" alt="Osiris Database Query" border="0"></p>
To define your query perform these steps:
<br>

<li>Under the <span class="menu">Retrieval Columns</span> section, select a project.</li>

<li>Then, select an assay from the updated assay menu. </li>

Note that the total numbers of available results are given in brackets after the 
assay names in the assay menu.<br>

<li>Select a <span class="menu">Result Column</span> (parameter) and click the 
<span class="menu">Add</span> button.</li>

Your selection will appear as an item in the column list on the right hand side 
of the <span class="menu">Retrieval Columns</span> section. 
<li>Repeat the last three steps until all result columns of interest are listed.</li>

<p>In the <span class="menu">Search Criteria</span> section you may define additional criteria, e.g. 
  a biological lab journal, a date limit, etc. Moreover, you may add assay specific 
  criteria, e.g. retrieve only compounds, that were active in one assay, but inactive 
  in another.</p>
<p>Furthermore, if your current DataWarrior document contains selected <b>Actelion 
  numbers</b> or <b>Chem Lab Journal/External References</b>, you may retrieve 
  results for these compounds only.</p>
<p>Whatever search criteria you define, DataWarrior will first create an internal 
  list of Actelion batches and samples which satisfy these criteria. In a second 
  step it will retrieve <b>all</b> results of these compounds that fit into the 
  defined retrieval columns. This has two implications: The search criteria are 
  independent from the retrieval columns. Thus, you may retrieve assay results 
  of compounds that are active in a different assay. Also, you may find results 
  that don't meet the original search criteria, e.g. if a batch was tested more 
  than once in a certain assay and at least one result meets the criteria then 
  you will see all results of this batch in the specified assay.<br>
</p>
<p>Once the query is defined you may just run it by clicking the <span class="menu">OK</span> button 
  or you may save it <b>in the database</b> for later reuse by clicking on the 
  <span class="menu">Save...</span> button. A dialog opens where you need to specify a name for your 
  query. In addition you may define your query public, which will allow other 
  users to see and run your query.</p>
<p></p>
<p>If you want to automatically apply certain view and filter settings to the 
  data after running a stored query, then you need to attach a Template to that 
  query. In order to do so, you need to run the query once, create and modify 
  views and filters, so that DataWarrior presents your data to your liking. Then 
  select <span class="menu">Assign Template To Query...</span> from the 
  <span class="keyword">OSIRIS Database</span> menu, 
  select your query name and click <span class="menu">OK</span>.</p>
<p>Do not confuse an <span class="keyword">Osiris Query</span> with an 
  <span class="keyword">Osiris Query File</span> (see below)!!!
</p>
<br><br>
<h3><i><a name="OsirisQueryFile"></a>Osiris Query Files</i></h3>

<p> An <span class="keyword">Osiris Query File</span> is the preferred way of sharing your new data 
  within the company. It is a small parameter file containing no information about 
  your results (thus very secure) but will retrieve information from the database 
  when you open it with DataWarrior. It will also reconstruct all view and filter 
  settings according to your formatting.</p>

<b>How to create an <span class="keyword">Osiris Query File?</span></b><br>

<p> First, define a query as describe before and retrieve the data form the database.<br>
  Format the results for the recipients as meaningful as possible by:<br>
</p>
<ul>
  <li>Get rid of 2D and 3D-views (right mouse-click on view name and select <span class="menu">Close 
    View</span>) if you don't use them to present certain aspects of your data.</li>
  <li>Rename views where appropriate (right mouse-click on view name and select 
    <span class="menu">Rename View...</span>).</li>
  <li>Use short meaningful column aliases as "IC50hPlasma" rather than "IC50hPlasma.Concentration" 
    (this can be done in the <span class="keyword">Table View</span> with a right mouse-click on the 
    column header and selecting <span class="menu">Set Column Alias...</span>).</li>
  <li>Add labels to the <span class="keyword">Structure View</span> showing for example the Actelion 
    No and important numerical data.</li>
</ul>
<p>Then, from the <span class="menu">File</span> menu, select <span class="menu">Save Special... / OSIRIS 
  Query</span>. Choose an meaningful name for the query file like "Recent Results 
  Assay xxx.dwaq".</p>
<p> When the recipient of such a query file launches it, he will first be asked 
  for the Osiris database user-ID and password. Afterwards the query is processed 
  and the data presented as you have defined it. The following picture illustrates 
  this. </p>

<p><b>Tip!:</b> If you need to report new assay results on a regular basis, then 
  you may construct a query that retrieves the most recent results and send the 
  same unchanged query file to your customers whenever new results were uploaded 
  to the database. Therefore select in the Osiris Database Query dialog, under 
  the option <span class="menu">Experiment/Calculation Date</span> the criteria 
  <span class="menu">most recent only</span>.
</p><br><br>
<h3><i><a name="Inventory"></a>Chemicals Inventory</i></h3>
<p> The menu item <span class="menu">Chemicals Inventory / Retrieve Data...</span> opens a dialog 
  that lets you chemicals and associated data from Actelion Chemicals Inventory 
  database, which contains in-house chemicals and their locations. You may search 
  by structure, location, registration user or date, and restrict result to empty 
  or not-empty bottles.</p>
<p>Provided you have a list of compounds, in order to check which of the compounds 
  are currently available in the Inventory you may select <span class="menu">Find 
  Matching Structures...</span> from the <span class="menu">Database 
  / Chemicals Inventory</span> menu, which performs an exact structure search 
  with every one of your compounds against the Inventory and retrieves Inventory 
  barcodes and the bottle locations of found chemicals into new columns of your 
  data.<br>
  <br>
</p>

<h3><i><a name="ProteinXtalDB"></a>The
Protein Crystallography Database</i></h3>

<p> Actelion's protein crystallography database houses experimental conditions 
  and parameters of our attempts to crystallize proteins in order to obtain high 
  resolution x-ray structures. Some observations are accompanied by photos of 
  promising crystals. To access this database select <span class="menu">Retrieve Protein Xtal 
  data...</span> from the Database menu. A dialog opens where you first need to select 
  a retrieval target among plate observation, experimental conditions, or plate 
  data. Then you should specify some search criteria and you may change the default 
  selection of columns to retrieve, which is specific to your retrieval target. 
</p>
<p> After retrieving observations one column is named '#image#'. This contains 
  a name of the observation image, if available. In this case the <span class="keyword">Detail View</span> 
  or <span class="keyword">Form View</span> display the associated image, of which you may enlarge a 
  section the see more details.</p>

<br>

<i>Example:</i><br>
<table class="wspace">
  <tr>
    <td class="wspace"><img src="help/img/actelion/XtalLowResPicture.jpg"></td>
    <td class="wspace">On the picture, define a rectangular area to enlarge by clicking and dragging 
      with the mouse.</td>
  </tr>
  <tr>
    <td class="wspace"><img src="help/img/actelion/XtalHighResPicture.jpg"></td>
    <td class="wspace">As soon as you release the mouse, DataWarrior will retrieve an higher 
      resolution picture and display the selected area within the available space.</td>
  </tr>
</table>
<p><br>
  <br>
</p>

<h3><i><a name="ExpressionDB"></a>The
Gene Expression Database</i></h3>

<p>
Actelion's in-house gene expression database comprises gene
expression values of various genes in various tissues.<br>

To access Gene Expression Data, select from the <span class="menu">Database</span> menu <span class="menu">
Retrieve Gene Expression Data</span>.
<br><br>

<h3><a name="CCDB"></a>Commercial Chemicals Database</h3>
<p>Actelion maintains a dedicated database of commercially available chemicals, being comparable
to MDL's ACD or CambridgeSoft's ACX databases. You may run a substructure or similarity search 
or/and limit your search to a specific list of supplier. If you don't specify any search criteria
you will retrieve the entire database with hundred thousands of rows.</p>
<p align="center"><img src="help/img/actelion/CCQuery.jpg"></p>
<br><br>

<h3><a name="HTSDB"></a>Screening Compounds Database </h3>
<p>Actelion maintains a dedicated server and database with the structures of commercially 
  available screening compounds. You may run substructure or similarity search 
  against this database by specifying a fragments or molecule's structure, 
  respectively. Alternatively, you may also select some structures of an open 
  DataWarrior document and perform a similarity search of all these structures 
  in one run. This might be useful, for instance, to check if there are screening 
  compounds commercially available that are similar to any of the lead compounds 
  of a certain project.</p>
<p align="center"><img src="help/img/actelion/HTSQuery.jpg"></p>

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